Published in Syst Biol on August 06, 2013
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol (2014) 1.21
The inference of gene trees with species trees. Syst Biol (2014) 0.97
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
Inferring horizontal gene transfer. PLoS Comput Biol (2015) 0.88
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Philos Trans R Soc Lond B Biol Sci (2015) 0.86
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics (2013) 0.85
Quantifying MCMC exploration of phylogenetic tree space. Syst Biol (2015) 0.84
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated. Mol Biol Evol (2015) 0.83
Joint amalgamation of most parsimonious reconciled gene trees. Bioinformatics (2014) 0.81
Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Mol Biol Evol (2014) 0.81
Polytomy refinement for the correction of dubious duplications in gene trees. Bioinformatics (2014) 0.80
Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci U S A (2017) 0.79
A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol (2014) 0.78
Phylogenetics and the human microbiome. Syst Biol (2014) 0.78
Cophylogeny reconstruction via an approximate Bayesian computation. Syst Biol (2014) 0.77
Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes. BMC Evol Biol (2017) 0.76
Efficient Gene Tree Correction Guided by Genome Evolution. PLoS One (2016) 0.75
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun (2017) 0.75
Exploring the space of gene/species reconciliations with transfers. J Math Biol (2014) 0.75
The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis. Genome Biol Evol (2015) 0.75
Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family. BMC Bioinformatics (2017) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96
An improved general amino acid replacement matrix. Mol Biol Evol (2008) 9.36
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics (2009) 6.74
High-resolution species trees without concatenation. Proc Natl Acad Sci U S A (2007) 4.44
Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol (2007) 4.13
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics (2006) 2.77
Rapid evolutionary innovation during an Archaean genetic expansion. Nature (2010) 2.34
Guided tree topology proposals for Bayesian phylogenetic inference. Syst Biol (2011) 2.32
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A (2009) 2.25
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc Natl Acad Sci U S A (2012) 1.66
Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res (2012) 1.44
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol (2008) 1.41
Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol Biol Evol (2011) 1.26
Dating the cyanobacterial ancestor of the chloroplast. ISME J (2010) 1.14
Genomes as documents of evolutionary history. Trends Ecol Evol (2009) 1.13
Lateral gene transfer from the dead. Syst Biol (2013) 1.10
TreeFix: statistically informed gene tree error correction using species trees. Syst Biol (2012) 1.03
Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol Biol (2012) 1.01
The estimation of tree posterior probabilities using conditional clade probability distributions. Syst Biol (2013) 0.95
Birth-death prior on phylogeny and speed dating. BMC Evol Biol (2008) 0.85
Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol (2008) 5.31
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol (2003) 4.47
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res (2006) 3.53
Evolutionary origins of genomic repertoires in bacteria. PLoS Biol (2005) 3.43
Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci U S A (2005) 2.28
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci (2010) 1.66
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc Natl Acad Sci U S A (2012) 1.66
Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci (2008) 1.64
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform (2011) 1.50
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol (2008) 1.41
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol (2010) 1.40
Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A (2012) 1.40
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics (2009) 1.31
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res (2009) 1.29
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics (2010) 1.24
Bio++: efficient extensible libraries and tools for computational molecular evolution. Mol Biol Evol (2013) 1.23
Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics (2008) 1.22
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol (2008) 1.15
Comparative genomics and the evolution of prokaryotes. Trends Microbiol (2007) 1.14
Genomes as documents of evolutionary history. Trends Ecol Evol (2009) 1.13
Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes. Genome Biol Evol (2009) 1.11
Lateral gene transfer from the dead. Syst Biol (2013) 1.10
Exploring the solution space of sorting by reversals, with experiments and an application to evolution. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.08
Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics (2012) 1.07
Reconstructing the architecture of the ancestral amniote genome. Bioinformatics (2011) 1.05
Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol Biol (2012) 1.01
Evolution under reversals: parsimony and conservation of common intervals. IEEE/ACM Trans Comput Biol Bioinform (2007) 1.00
"Orphan" retrogenes in the human genome. Mol Biol Evol (2012) 1.00
ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics (2012) 0.99
Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol (2011) 0.98
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol Biol Evol (2003) 0.96
Yeast ancestral genome reconstructions: the possibilities of computational methods II. J Comput Biol (2010) 0.95
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event? BMC Evol Biol (2008) 0.94
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
A Bayesian method for analyzing lateral gene transfer. Syst Biol (2014) 0.93
Cassis: detection of genomic rearrangement breakpoints. Bioinformatics (2010) 0.92
A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS One (2012) 0.92
FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics (2013) 0.91
Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS One (2012) 0.89
Efficient selection of branch-specific models of sequence evolution. Mol Biol Evol (2012) 0.87
Bayesian sampling of genomic rearrangement scenarios via double cut and join. Bioinformatics (2010) 0.87
Moments of genome evolution by Double Cut-and-Join. BMC Bioinformatics (2015) 0.87
Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene. PLoS One (2011) 0.87
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol (2014) 0.86
Drift and genome complexity revisited. PLoS Genet (2011) 0.86
Linearization of ancestral multichromosomal genomes. BMC Bioinformatics (2012) 0.85
Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test. Mol Phylogenet Evol (2004) 0.85
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics (2013) 0.85
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem. Bioinformatics (2011) 0.83
An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution (2012) 0.79
A bunch of fun-guys: the whole-genome view of yeast evolution. Trends Genet (2005) 0.79
Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes. J Comput Biol (2009) 0.78
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies. BMC Bioinformatics (2015) 0.77
TPMS: a set of utilities for querying collections of gene trees. BMC Bioinformatics (2013) 0.77
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. BMC Genomics (2013) 0.77
The molecular signal for the adaptation to cold temperature during early life on Earth. Biol Lett (2013) 0.77
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. BMC Genomics (2015) 0.77
Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics (2015) 0.76
[Healing the tree of life with lateral gene transfers]. Med Sci (Paris) (2012) 0.75
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. Pac Symp Biocomput (2010) 0.75